The Salivary Mycobiome Contains 2 Ecologically Distinct Mycotypes.

A broad range of fungi has been detected in molecular surveys of the oral mycobiome. However, knowledge is still lacking on interindividual variability of these communities and the ecologic and clinical significance of oral fungal commensals. In this cross-sectional study, we use internal transcribed spacer 1 amplicon sequencing to evaluate the salivary mycobiome in 59 subjects, 36 of whom were scheduled to receive cancer chemotherapy.

Integrated Analysis of Clinical and Microbiome Risk Factors Associated with the Development of Oral Candidiasis during Cancer Chemotherapy.

Oral candidiasis is a common side effect of cancer chemotherapy. To better understand predisposing factors, we followed forty-five subjects who received 5-fluorouracil- or doxorubicin-based treatment, during one chemotherapy cycle. Subjects were evaluated at baseline, prior to the first infusion, and at three additional visits within a two-week window.

Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis.

Background: Gastrointestinal mucosal injury (mucositis), commonly affecting the oral cavity, is a clinically significant yet incompletely understood complication of cancer chemotherapy. Although antineoplastic cytotoxicity constitutes the primary injury trigger, the interaction of oral microbial commensals with mucosal tissues could modify the response. It is not clear, however, whether chemotherapy and its associated treatments affect oral microbial communities disrupting the homeostatic balance between resident microorganisms and the adjacent mucosa and if such alterations are associated with mucositis.

Mining the oral mycobiome: Methods, components, and meaning.

Research on oral fungi has centered on Candida. However, recent internal transcribed spacer (ITS)-based studies revealed a vast number of fungal taxa as potential oral residents. We review DNA-based studies of the oral mycobiome and contrast them with cultivation-based surveys, showing that most genera encountered by cultivation have also been detected molecularly.

End stage renal disease as a modifier of the periodontal microbiome.

Background: Evidence supports high prevalence of periodontitis in patients with chronic kidney disease. Several renal factors have been proposed as possible modifiers of periodontitis pathogenesis in this population. In this cross sectional study, we investigated whether distinct microbial profiles in renal patients could explain high periodontitis prevalence.

Microbiome profiles in periodontitis in relation to host and disease characteristics.

Periodontitis is an inflammatory condition that affects the supporting tissues surrounding teeth. The occurrence of periodontitis is associated with shifts in the structure of the communities that inhabit the gingival sulcus. Although great inter-subject variability in the subgingival microbiome has been observed in subjects with periodontitis, it is unclear whether distinct community types exist and if differences in microbial signatures correlate with host characteristics or with the variable clinical presentations of periodontitis.

Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench.

High throughput sequencing has accelerated knowledge on the oral microbiome. While the bacterial component of oral communities has been extensively characterized, the role of the fungal microbiota in the oral cavity is largely unknown. Interactions among fungi and bacteria are likely to influence oral health as exemplified by the synergistic relationship between Candida albicans and oral streptococci.

Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing.

Background And Objective: The advent of next-generation sequencing has significantly facilitated characterization of the oral microbiome. Despite great efforts in streamlining the processes of sequencing and data curation, upstream steps required for amplicon library generation could still influence 16S rRNA gene-based microbial profiles. Among upstream processes, DNA extraction is a critical step that could represent a great source of bias.

Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal.

Fungi are a large, complex group, increasingly recognized as emerging threats. Their roles as modifiers of health mandate accurate portrayals of fungal communities in humans. As an entry point into the airways and gastrointestinal tract, fungi in the mouth are relevant to several biocompartments.

Routine use of the Ion Torrent AmpliSeq™ Cancer Hotspot Panel for identification of clinically actionable somatic mutations.

Background: Somatic mutation analysis is standard of practice for solid tumors in order to identify therapeutic sensitizing and resistance mutations. Our laboratory routinely performed standalone PCR-based methods for mutations in several genes. Rapid discovery and introduction of new therapeutics has demanded additional genomic information for adequate management of the cancer patient.

Transplantation-associated long-term immunosuppression promotes oral colonization by potentially opportunistic pathogens without impacting other members of the salivary bacteriome.

Solid-organ transplant recipients rely on pharmacological immunosuppression to prevent allograft rejection. The effect of such chronic immunosuppression on the microflora at mucosal surfaces is not known. We evaluated the salivary bacterial microbiome of 20 transplant recipients and 19 nonimmunosuppressed controls via 454 pyrosequencing of 16S rRNA gene amplicons.

The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation.

The goals of this study were to better understand the ecology of oral subgingival communities in health and periodontitis and elucidate the relationship between inflammation and the subgingival microbiome. Accordingly, we used 454-pyrosequencing of 16S rRNA gene libraries and quantitative PCR to characterize the subgingival microbiome of 22 subjects with chronic periodontitis. Each subject was sampled at two sites with similar periodontal destruction but differing in the presence of bleeding, a clinical indicator of increased inflammation.

Using high throughput sequencing to explore the biodiversity in oral bacterial communities.

High throughput sequencing of 16S ribosomal RNA gene amplicons is a cost-effective method for characterization of oral bacterial communities. However, before undertaking large-scale studies, it is necessary to understand the technique-associated limitations and intrinsic variability of the oral ecosystem. In this work we evaluated bias in species representation using an in vitro-assembled mock community of oral bacteria.

Measuring acceptable treatment failure rates for community-acquired pneumonia: potential for reducing duration of treatment and antimicrobial resistance.

Objective: This study was designed to establish the rates of treatment failure for community-acquired pneumonia that are acceptable to knowledgeable and experienced physicians, in order to facilitate the interpretation of existing studies and the design of new studies aimed at optimizing the duration of antibiotic therapy. Reducing the duration of antibiotic therapy is one strategy for reducing antibiotic exposure and thereby minimizing the potential for the emergence of antimicrobial resistance.

Design: Survey soliciting the acceptable failure rate for treatment given to an adult patient with uncomplicated community-acquired pneumonia treated with standard-of-care therapy in the outpatient setting.

Use of decolonization to prevent staphylococcal infections in various healthcare settings: results of an Emerging Infections Network survey.

Less than 20% of infectious diseases consultants work in hospitals that routinely employ decolonization therapy for individuals with staphylococcal carriage undergoing elective surgical procedures or for infection control efforts to limit nosocomial transmission of methicillin-resistant Staphylococcus aureus (MRSA). However, infectious diseases consultants frequently encounter patients with recurrent MRSA furunculosis and attempt to decolonize them.

Bacterial infections associated with blood transfusion: experience and perspective of infectious diseases consultants.

Background: On March 1, 2004, the AABB adopted a new standard that requires member blood banks and transfusion services to implement measures to limit and detect bacterial contamination in all platelet (PLT) components. The AABB has since developed several guidelines to assist blood transfusion services and blood banks in this area, some of which are relevant to clinical practice. Knowledge and experience among clinicians (including infectious disease consultants, who can play an important role in managing patients with sepsis) concerning risk of bacterial infections associated with transfusion, however, are unknown.

Experience of infectious diseases consultants with outpatient parenteral antimicrobial therapy: results of an emerging infections network survey.

Background: Despite the increasing use of outpatient parenteral antimicrobial therapy (OPAT), little is known about the role of infectious diseases consultants in the process or their perceptions of OPAT.

Methods: In May 2004, the Infectious Diseases Society of America Emerging Infections Network (EIN) surveyed its members to characterize their involvement and experiences with OPAT.

Results: Of the 454 respondents (54%) who completed the questionnaire, 426 (94%) indicated that patients in their primary inpatient facility were "frequently" discharged while receiving OPAT, estimating that, on average, 19 patients are discharged from their hospitals while receiving OPAT each month.

A national survey of the Infectious Diseases Society of America Emerging Infections Network concerning neuraminidase inhibitor prescription practices and pandemic influenza preparations.

This report summarizes the findings of a national survey of infectious diseases consultants regarding their use of neuraminidase inhibitors and the status of their planning for an influenza pandemic. The respondents indicated that government stockpiles should be increased, that many have received requests for antiviral medications, and that additional recommendations regarding the appropriate use of antiviral medications would be helpful.

Preventing transmission of multidrug-resistant bacteria in health care settings: a tale of 2 guidelines.

Two guidelines for the control of multidrug-resistant organisms in health care facilities have appeared during the past 3 years--one from the Society for Healthcare Epidemiology of America and one, in draft form, from the Healthcare Infection Control Practices Advisory Committee of the Centers for Disease Control and Prevention. These guidelines reflect universal concern in the infection-control community about today's unprecedented levels of activity of multidrug-resistant organisms and about inadequate or inconsistent application of potentially effective control measures. The 2 guidelines provide detailed reviews of pertinent issues and evidence-based, rated recommendations, which overlap considerably.

Physicians' acceptable treatment failure rates in antibiotic therapy for coagulase-negative staphylococcal catheter-associated bacteremia: implications for reducing treatment duration.

Background: Decreasing the duration of antimicrobial therapy is an attractive strategy for delaying the emergence of antimicrobial resistance. Limited data regarding optimal treatment durations for most clinical infections hinder the adoption of this approach and impair optimal physician-patient communication under the shared decision-making model. We aimed to identify acceptable failure rates among infectious disease consultants (IDCs) for treatment of central venous catheter-associated bacteremia.

A national survey of severe influenza-associated complications among children and adults, 2003-2004.

This report summarizes findings of a national survey conducted among infectious diseases consultants to assess complications associated with influenza during the 2003-2004 influenza season. The survey identified severe complications, including secondary infection with Staphylococcus aureus and deaths among children and adults, as well as perceived shortages in rapid diagnostic tests and influenza vaccine.

Management of inpatients colonized or infected with antimicrobial-resistant bacteria in hospitals in the United States.

Background: Although guidelines for multidrug-resistant organisms generally include recommendations for contact precautions and surveillance cultures, it is not known how frequently U.S. hospitals implement these measures on a routine basis and whether infectious diseases consultants endorse their use.

An organizational model of transcription factor binding sites for a histone promoter in D. melanogaster.

The Drosophila H2A-H2B histone spacer, a small region that functions as a bidirectional promoter for the gene pair, was used as a test sequence for generation of a computationally derived organizational model of transcription factor (TF) binding sites. Expression studies of the spacer revealed that it contains the necessary sequences to confer replication-dependent transcription in partially synchronized cells in culture. Informatics analysis of the spacer uncovered a number of binding sites for specific TFs, none of which had been previously associated with this particular promoter.